Figure 4.

Innate immune-related co-expression network generated using WGCNA and mitochondrial-related gene enrichment analysis. (A) Analysis of the scale-free fit index (upper left panel) and the mean connectivity for various soft-thresholding powers (upper right panel). Different colours represent different gene modules (lower panel). (B) Hierarchical clustering correlation among WGCNA modules. A total of 11 gene co-expression modules were identified. (C) Heatmap demonstrating module–trait relationships. Green indicates a positive correlation and orange indicates a negative correlation between the expression of genes in the modules and the abundance of innate immune cells. The number in each immune cell indicates the correlation coefficient and p-value. (D, E) Bar graph demonstrating the results of GO functional annotation analysis performed using Metascape in the brown (D) and blue (E) modules. (F) Significantly enriched clusters marked in different colours in the network were annotated using Metascape (left panel). Different colours represent different GO terms. The Venn diagram (right panel) demonstrates the 561 overlapping genes between mitochondria-related genes and genes in the brown and blue modules. (G) Heatmap demonstrating functional categories in three innate immune cell types (different modules) as identified using Proteomaps (www.proteomaps.net). Each protein encoded by a known ID gene is represented by a polygon, and functionally related proteins are arranged in common and similar regions.